Comparison between the ages for the genders and types¶
Questions
- What are the differences between the ages for the different combinations of gender and types?
- Do we observe the same changes as globally?
Age effect - General Questions
- What are the differences between the ages?
- Which genes and pathways are differentially expressed between 8w and 52w, between 52w and 104w, between 8w and 104w? Are they the same? Is there a gradient?
- Are they different for the two genders?
- Are they different for the two types?
Warning message in is.na(x[[i]]): “is.na() applied to non-(list or vector) of type 'environment'”Warning message in rsqlite_fetch(res@ptr, n = n): “Don't need to call dbFetch() for statements, only for queries”
========================================================================== * * Package WGCNA 1.63 loaded. * * Important note: It appears that your system supports multi-threading, * but it is not enabled within WGCNA in R. * To allow multi-threading within WGCNA with all available cores, use * * allowWGCNAThreads() * * within R. Use disableWGCNAThreads() to disable threading if necessary. * Alternatively, set the following environment variable on your system: * * ALLOW_WGCNA_THREADS=<number_of_processors> * * for example * * ALLOW_WGCNA_THREADS=4 * * To set the environment variable in linux bash shell, type * * export ALLOW_WGCNA_THREADS=4 * * before running R. Other operating systems or shells will * have a similar command to achieve the same aim. * ========================================================================== Allowing multi-threading with up to 4 threads. [1] "preparing gene to GO mapping data..." [1] "preparing IC data..." [1] "preparing gene to GO mapping data..." [1] "preparing IC data..." [1] "preparing gene to GO mapping data..." [1] "preparing IC data..."
Data¶
Stats¶
| Wald padj < 0.05 | LFC > 0 (Wald padj < 0.05) | LFC < 0 (Wald padj < 0.05) | |
|---|---|---|---|
| 52w VS 8w (F, SPF) | 1799 | 1038 | 761 |
| 52w VS 8w (F, GF) | 1026 | 635 | 391 |
| 52w VS 8w (M, SPF) | 367 | 246 | 121 |
| 52w VS 8w (M, GF) | 230 | 126 | 104 |
| 104w VS 52w (F, SPF) | 216 | 117 | 99 |
| 104w VS 52w (F, GF) | 449 | 231 | 218 |
| 104w VS 52w (M, SPF) | 3428 | 1845 | 1583 |
| 104w VS 52w (M, GF) | 2747 | 1379 | 1368 |
| 104w VS 8w (F, SPF) | 2004 | 1109 | 895 |
| 104w VS 8w (F, GF) | 1428 | 772 | 656 |
| 104w VS 8w (M, SPF) | 3863 | 2069 | 1794 |
| 104w VS 8w (M, GF) | 2340 | 1195 | 1145 |
Differentially expressed genes¶
52w VS 8w (F, SPF) 52w VS 8w (F, GF) 52w VS 8w (M, SPF)
0.5158421 0.5068226 0.6512262
52w VS 8w (M, GF) 104w VS 52w (F, SPF) 104w VS 52w (F, GF)
0.7869565 0.6712963 0.6570156
104w VS 52w (M, SPF) 104w VS 52w (M, GF) 104w VS 8w (F, SPF)
0.3856476 0.6308700 0.5813373
104w VS 8w (F, GF) 104w VS 8w (M, SPF) 104w VS 8w (M, GF)
0.6484594 0.5034947 0.6700855
Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in stack.default(getgo(rownames(l$deg), "mm10", "geneSymbol")): “non-vector elements will be ignored”Warning message in stack.default(getgo(rownames(as.data.frame(l$deg)), "mm10", "geneSymbol", : “non-vector elements will be ignored”
Comparison of the numbers per types¶
DEG into gene co-expression network¶
- White: up-regulated
- Black: down-regulated
52w VS 8w¶
| 52w VS 8w | M | F |
|---|---|---|
| SPF | ||
| GF |
104w VS 52w¶
| 104w VS 52w | M | F |
|---|---|---|
| SPF | ||
| GF |
GO analysis¶
Biological process¶
Dot-plot with the most over-represented BP GO (20 most significant p-values for the different comparison)
Using term, id as id variables Using term, id as id variables
Network based on description similarity
52w VS 8w¶
| 52w VS 8w | M | F |
|---|---|---|
| SPF | ||
| GF |
104w VS 52w¶
| 104w VS 52w | M | F |
|---|---|---|
| SPF | ||
| GF |
Cellular components¶
Dot-plot with the most over-represented CC GO (20 most significant p-values for the different comparison)
Using term, id as id variables Using term, id as id variables
Molecular functions¶
Dot-plot with the most over-represented MF GO (20 most significant p-values for the different comparison)
Using term, id as id variables Using term, id as id variables
KEGG pathways¶
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[1] "Note: 12 of 7590 unique input IDs unmapped."
[1] "Note: 12 of 7590 unique input IDs unmapped."
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Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. 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Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”
[1] "Note: 12 of 7590 unique input IDs unmapped." [1] "Note: 12 of 7590 unique input IDs unmapped."
Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”
[1] "Note: 12 of 7590 unique input IDs unmapped."
Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”
[1] "Note: 12 of 7590 unique input IDs unmapped."
Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”
[1] "Note: 12 of 7590 unique input IDs unmapped."
Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”
[1] "Note: 12 of 7590 unique input IDs unmapped."
What happen to SPF aging genes in GF?¶
Genes:
- Set 52w vs 8w: 52w != 8w (SPF)
- Set 104w vs 52w: 104w != 52w (SPF)
- Set all: 52w != 8w (SPF) and 104w != 52w (SPF)
Female¶
Genes in "../results/dge/age-effect/age_type_gender/spf_f_aging_genes"
- deg_52w_vs_8w
- 1799
- deg_104w_vs_52w
- 216
- deg_52w_vs_8w_and_104w_vs_52w
- 54
No trace type specified: Based on info supplied, a 'scatter' trace seems appropriate. Read more about this trace type -> https://plot.ly/r/reference/#scatter Warning message: “Ignoring 252 observations”No trace type specified: Based on info supplied, a 'scatter' trace seems appropriate. Read more about this trace type -> https://plot.ly/r/reference/#scatter Warning message: “Ignoring 3341 observations”No trace type specified: Based on info supplied, a 'scatter' trace seems appropriate. Read more about this trace type -> https://plot.ly/r/reference/#scatter Warning message: “Ignoring 241 observations”No trace type specified: Based on info supplied, a 'scatter' trace seems appropriate. Read more about this trace type -> https://plot.ly/r/reference/#scatter Warning message: “Ignoring 1901 observations”
Male¶
Genes in "../results/dge/age-effect/age_type_gender/spf_m_aging_genes"
- deg_52w_vs_8w
- 367
- deg_104w_vs_52w
- 3428
- deg_52w_vs_8w_and_104w_vs_52w
- 155
No trace type specified: Based on info supplied, a 'scatter' trace seems appropriate. Read more about this trace type -> https://plot.ly/r/reference/#scatter Warning message: “Ignoring 252 observations”No trace type specified: Based on info supplied, a 'scatter' trace seems appropriate. Read more about this trace type -> https://plot.ly/r/reference/#scatter Warning message: “Ignoring 3341 observations”No trace type specified: Based on info supplied, a 'scatter' trace seems appropriate. Read more about this trace type -> https://plot.ly/r/reference/#scatter Warning message: “Ignoring 241 observations”No trace type specified: Based on info supplied, a 'scatter' trace seems appropriate. Read more about this trace type -> https://plot.ly/r/reference/#scatter Warning message: “Ignoring 1901 observations”